LAMMPS (11 Aug 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
  using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Langevin)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.toluene extra/special/per/atom 1
  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
  2 by 1 by 2 MPI processor grid
  reading atoms ...
  5500 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  8 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  reading bonds ...
  5500 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6000 dihedrals
  reading impropers ...
  1500 impropers
  5 = max # of 1-2 neighbors
  10 = max # of 1-3 neighbors
  16 = max # of 1-4 neighbors
  20 = max # of special neighbors

comm_modify vel yes

group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES

pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT

neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C C C C N N D D D D D

fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
  1250 = # of size 2 clusters
  0 = # of size 3 clusters
  250 = # of size 4 clusters
  0 = # of frozen angles

fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nve

compute cTEMP all temp/drude

thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.382011
  grid = 40 40 40
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0325934
  estimated relative force accuracy = 9.8154e-05
  using double precision FFTs
  3d grid and FFT values/proc = 34263 16000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 8 8 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/thole/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
       0            0    14386.197    2910.7282    202.07402    11475.469    6565.4851    20.333365 1.0706727e-06 1.3894617e-07    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
      50    1.0658228    8014.6879    4671.7498    324.33095    3342.9381    1798.7991    670.22837    651.99307    50.352024    819.34616    1305984.9   -1306632.7    17255.952    48631.318    442.52888    116.12397 
     100     2.136163    6185.5007    3697.0414    256.66292    2488.4593    974.42931    774.88353    840.46625    66.896007    427.27085    1306105.5     -1306701    15044.739    48631.318    381.93582    35.802658 
     150     3.202647    5418.0644    3628.2714    251.88864    1789.7929    764.02696    804.61034    641.14915    47.995428    108.05084    1306138.9   -1306714.9    15258.194    48631.318    388.65363    10.777816 
     200    4.2728949    4838.4235    3303.8964    229.36927    1534.5271    702.10438    772.85348    625.99718    52.299187   -63.792745    1306166.5   -1306721.4    13487.722    48631.318    357.35337    3.7423617 
     250    5.3275268    4461.2438    3084.8973    214.16551    1376.3465    693.85145    823.23815    599.85313    48.280277   -230.56822    1306167.8   -1306726.1    8779.0061    48631.318    334.59262    1.8620294 
     300    6.3794398    4179.6462    2885.0738    200.29299    1294.5724      739.337    868.84011    555.04912    44.838819   -354.73738    1306171.3     -1306730    4410.8735    48631.318    313.17473    1.2892347 
     350     7.427706    3934.3968    2756.2421    191.34899    1178.1546    666.16877    877.32996    548.99846    45.087026   -404.32209      1306179   -1306734.1    8477.8828    48631.318    299.22663    1.1698531 
     400    8.4820418    3800.4769    2674.8317    185.69716    1125.6452    693.29433    841.29833    579.61438    48.325361   -470.18802    1306170.5   -1306737.2    6265.7532    48631.318    290.39105    1.1303952 
     450     9.528651      3685.28    2616.9074    181.67583    1068.3726    702.68328    886.66644    555.74511    46.160811   -557.70651    1306176.6   -1306741.7    2701.7737    48631.318    284.11064     1.091646 
     500    10.579133    3582.6591    2517.6443    174.78461    1065.0148    701.82101     894.9429    554.06012    46.074357   -570.49878    1306181.8   -1306743.2    3643.7426    48631.318    273.31525    1.0831346 
     550    11.629649    3542.0402    2527.0386     175.4368    1015.0016    688.73877     916.2381    521.69932    44.014375   -580.05437      1306171   -1306746.6    2928.6632    48631.318    274.34257    1.0740018 
     600    12.684143    3507.0443    2519.9749    174.94641    987.06936    711.58734    894.63276    525.57884    42.944226   -603.24423    1306161.2   -1306745.7    2082.9907    48631.318    273.57124    1.0784841 
     650    13.737965    3416.2001    2445.9361    169.80635    970.26394    706.95207    891.76446    540.90369    45.970985   -626.32832    1306160.2   -1306749.2    1912.8783    48631.318     265.5023    1.1021764 
     700    14.777375    3419.7572     2446.117    169.81891    973.64019    664.17579    936.51992    551.67148    45.696531   -634.70926    1306159.6   -1306749.4    2215.7085    48631.318    265.53614    1.0774684 
     750    15.795347    3418.6537     2449.343    170.04287    969.31069    706.12432    899.61553    553.21874    45.793213   -642.75298    1306158.1   -1306750.8    1022.2516    48631.318    265.89304    1.0681488 
     800    16.835794    3385.2449    2465.4963    171.16429    919.74864    692.34918    888.91243    530.24204    45.132243   -638.54787    1306154.6     -1306753    1601.1391    48631.318    267.64361    1.0797553 
     850     17.87536    3397.1124    2426.3129    168.44403    970.79951    717.48898    878.71057    580.26487    46.675101   -646.96926    1306150.9   -1306756.3    1048.7905    48631.318    263.38063    1.0785255 
     900    18.899639    3324.2064    2447.5004    169.91495    876.70599    683.62339    881.77789    531.98758    43.646731   -648.59248    1306144.4   -1306760.2    2221.5859    48631.318    265.69596    1.0608373 
     950    19.938468    3316.6329    2398.6988    166.52695    917.93405    702.84237    885.96473    540.35376    45.671318   -638.80334    1306144.4   -1306762.5    1955.2237    48631.318    260.38167    1.0687233 
    1000    20.973543    3287.4205     2384.191    165.51976    903.22949    705.56988    889.96387    535.23674    44.902139   -661.28175    1306150.4   -1306761.6    90.200683    48631.318    258.81506    1.0477545 
    1050    21.990961    3297.7806    2392.0372    166.06448    905.74339    697.33157    889.75086     537.2395    46.319713   -636.03286    1306135.9   -1306764.8    1893.8234    48631.318    259.67633    1.0344207 
    1100    23.006456     3240.651    2370.2217    164.54996    870.42931    693.87289     897.0846    526.89184    43.778979   -657.83716    1306132.1   -1306765.5    799.62979    48631.318    257.28711    1.0618941 
    1150    24.014558     3232.457    2377.9797    165.08855    854.47728    692.51558    897.77048     520.3269    43.903959   -657.38369    1306126.9   -1306769.6    178.21408    48631.318    258.13876    1.0479172 
    1200    25.010178    3238.4266    2392.0623    166.06622    846.36427    695.98996      887.237    522.01974    42.355716   -660.92843    1306124.7     -1306765    1006.1877    48631.318    259.66037    1.0698925 
    1250     26.01949    3198.3364    2332.7551    161.94888    865.58134    690.81786    897.35028    524.47996    44.421121   -640.92419    1306116.3   -1306766.8    2073.9672    48631.318      253.227    1.0326937 
    1300    27.026911    3237.6809    2386.3739    165.67131    851.30706    672.11785    901.04813     530.2964    44.020263   -655.33033    1306125.7   -1306766.5    579.46013    48631.318    259.05838    1.0374113 
    1350    28.033721    3285.9536     2371.155    164.61476    914.79862    718.12968    928.41764    524.02349     43.89896   -657.10221    1306127.3   -1306769.9    518.88041    48631.318    257.36737    1.0993197 
    1400    29.026742    3272.2173    2391.4158    166.02134    880.80147    712.59883    896.13616    532.95785    45.989768   -658.37495    1306125.6   -1306774.1     961.2067    48631.318     259.5968    1.0557033 
    1450    30.032566    3244.2627    2356.0955    163.56926    888.16727    714.72692    901.18382    534.59787    45.517573   -655.58258    1306124.5   -1306776.8    596.10558    48631.318    255.75173     1.058657 
    1500     31.03878    3244.8598    2408.5382    167.21004    836.32161    695.63105    867.27743    527.37333    44.496971   -648.96393    1306125.2   -1306774.7    443.71088    48631.318    261.45495    1.0648973 
    1550    32.041435    3239.3658    2367.1336    164.33557    872.23223    704.16965     884.5938    544.41685    46.110791   -654.61963    1306124.1   -1306776.5    -446.5562    48631.318    256.96289    1.0409003 
    1600    33.058977    3221.4258    2334.2656    162.05375     887.1602     713.8296    885.80472    533.86753    45.413663   -633.58824    1306119.6   -1306777.8    1527.9489    48631.318    253.36367    1.0817678 
    1650    34.080875    3224.4472    2385.9055    165.63879    838.54168    681.01628    879.88017    536.75983    43.884394   -643.24788      1306114   -1306773.8    1314.2208    48631.318    258.97106    1.1033457 
    1700    35.095047    3178.6575    2352.4294    163.31475     826.2281    700.79494    854.06687    549.39826    46.155483   -662.57181    1306115.2   -1306776.9   -187.36898    48631.318    255.35015    1.0638209 
    1750    36.093828     3219.473    2371.9421     164.6694    847.53093    699.44953    891.26068    541.91687    45.714235   -679.13432    1306120.3   -1306771.9   -618.32924    48631.318    257.48034    1.0512601 
    1800    37.110101    3202.0094    2371.8909    164.66585    830.11842    698.44522    858.38216    550.82008    46.315893   -667.77838    1306119.2   -1306775.3   -9.4963278    48631.318    257.46873    1.0619052 
    1850    38.121337    3202.0111    2366.6984    164.30536    835.31277    714.69988     849.6778    553.24258    46.502994   -667.44162    1306114.9   -1306776.3    131.11108    48631.318    256.90165    1.0656162 
    1900    39.132607    3228.7805     2365.934    164.25229    862.84648    720.68418    890.65533    554.75943    45.736726   -685.52803    1306115.1   -1306778.5   -82.525994    48631.318    256.81451    1.0726218 
    1950    40.127507    3218.4068    2443.0023    169.60267    775.40452    673.40001    874.63022    529.69964    43.166847   -680.57322    1306115.4   -1306780.3    622.76654    48631.318    265.20173    1.0693092 
    2000    41.138176     3257.463    2375.6246    164.92505    881.83842    677.60747    933.47776    547.01076    46.507189   -665.56273    1306123.7   -1306780.9    1829.3477    48631.318    257.88171    1.0500311 
Loop time of 41.1383 on 4 procs for 2000 steps with 5500 atoms

Performance: 2.100 ns/day, 11.427 hours/ns, 48.617 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 21.082     | 22.483     | 24.145     |  26.6 | 54.65
Bond    | 4.9992     | 5.0781     | 5.1544     |   2.7 | 12.34
Kspace  | 9.1202     | 10.806     | 12.272     |  39.7 | 26.27
Neigh   | 0.45045    | 0.45076    | 0.45094    |   0.0 |  1.10
Comm    | 0.85982    | 0.87287    | 0.88725    |   1.2 |  2.12
Output  | 0.0036495  | 0.004005   | 0.0049655  |   0.9 |  0.01
Modify  | 1.4009     | 1.401      | 1.4013     |   0.0 |  3.41
Other   |            | 0.04245    |            |       |  0.10

Nlocal:    1375 ave 1398 max 1361 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost:    7745.75 ave 7788 max 7697 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs:    334374 ave 348629 max 319495 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 1337494
Ave neighs/atom = 243.181
Ave special neighs/atom = 15.6364
Neighbor list builds = 31
Dangerous builds = 0
Total wall time: 0:00:41
